2PP8 | pdb_00002pp8

Formate bound to oxidized wild type AfNiR

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.334	α = 90
b = 102.453	β = 90
c = 146.179	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2005-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.97	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.5	30		0.037		3.6		147552

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55			0.451		2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	30	126965	6670	90.3	0.16575	0.16391	0.16	0.20119	0.2	RANDOM	19.138

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.32			-1.03		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.972
r_dihedral_angle_4_deg	20.143
r_dihedral_angle_3_deg	12.16
r_dihedral_angle_1_deg	6.765
r_sphericity_free	3.825
r_scangle_it	2.68
r_sphericity_bonded	2.588
r_scbond_it	1.956
r_rigid_bond_restr	1.307
r_angle_refined_deg	1.288
r_mcangle_it	1.238
r_mcbond_it	0.904
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.216
r_nbd_refined	0.192
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7680
Nucleic Acid Atoms
Solvent Atoms	1098
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing